BLASTP 2.2.18 [Mar-02-2008] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Reference for compositional score matrix adjustment: Altschul, Stephen F., John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109. Query= 0040.0002.p (331 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310777|ref|YP_003774869.1| GGDEF family protein [Herbaspir... 514 e-147 gi|300310347|ref|YP_003774439.1| GGDEF domain transmembrane prot... 102 4e-23 gi|300313424|ref|YP_003777516.1| GGDEF domain-containing protein... 100 2e-22 gi|300312078|ref|YP_003776170.1| hypothetical protein Hsero_2767... 99 6e-22 gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodies... 98 9e-22 >gi|300310777|ref|YP_003774869.1| GGDEF family protein [Herbaspirillum seropedicae SmR1] Length = 352 Score = 514 bits (1323), Expect = e-147, Method: Compositional matrix adjust. Identities = 244/331 (73%), Positives = 281/331 (84%), Gaps = 6/331 (1%) Query: 7 AGAVITGLYELTKVKQIRVLDIFSLREEMFVQEKMYLNEGHLSTIAEHTEDDPKEPLSGY 66 A +V++ LY+LT VK IR++DIF++R+E +VQEKM + +G L TI EHT DDPKE LS Y Sbjct: 22 AISVVSALYQLTDVKTIRMMDIFTMRDEHYVQEKMVIRDGTLHTIDEHTADDPKELLSAY 81 Query: 67 PAIVECIRQHKNEHYEIAADGWHVLWLPVWLHGKVNTCLEIRHPHAYDTGTLELIDGIFG 126 PA+V CIR H NE+ E DG HVLWLPVWLHGK+N+CLEIR + +++I GIF Sbjct: 82 PAMVACIRNHLNEYLEATPDGLHVLWLPVWLHGKMNSCLEIRSQQPFAPQMMDVIHGIFH 141 Query: 127 IYCNYQSLLDYSERDALTGLFNRKTFDEQFSRHAFALAPHEAHSLDNNERRNGG------ 180 ++CNYQSLLDYSERDALTGLFNRKTFDEQF+R+AFA+APHEAHS++ +ERR+ Sbjct: 142 VFCNYQSLLDYSERDALTGLFNRKTFDEQFTRYAFAIAPHEAHSMEQDERRHDSAEAQDD 201 Query: 181 ETKAHWLAVVDIDHFKQVNDQFGHLYGDEVLILVANILRTSFRSHDRIFRFGGEEFVILL 240 E K HWLAVVDIDHFKQVND++GHLYGDEVLILVANILR SFRSHDRIFRFGGEEFVILL Sbjct: 202 EPKGHWLAVVDIDHFKQVNDRYGHLYGDEVLILVANILRASFRSHDRIFRFGGEEFVILL 261 Query: 241 RSTTLADASKIFDRFRQHVQEYDFPQVGKVTVSLGFVGISQETPVVILGHADQALYHAKK 300 RSTTL+DA KIFDRFRQ+VQEYDFPQVGKVTVSLGFVGI++ETPVVILGHADQALYHAKK Sbjct: 262 RSTTLSDARKIFDRFRQNVQEYDFPQVGKVTVSLGFVGIARETPVVILGHADQALYHAKK 321 Query: 301 NGRNRICYYDELVTSGVLSNEISTNDIVEFF 331 GRNRICYY ELV SGVL + I+TND VEFF Sbjct: 322 TGRNRICYYQELVNSGVLRSGIATNDTVEFF 352 >gi|300310347|ref|YP_003774439.1| GGDEF domain transmembrane protein [Herbaspirillum seropedicae SmR1] Length = 334 Score = 102 bits (254), Expect = 4e-23, Method: Compositional matrix adjust. Identities = 67/167 (40%), Positives = 90/167 (53%), Gaps = 16/167 (9%) Query: 141 DALTGLFNRKTFDEQFSRHAFALAPHEAHSLDNNERRNGGETKAHWLAVVDIDHFKQVND 200 D LTGL NR DE LDN R K L ++DIDHFK+VND Sbjct: 166 DKLTGLANRMKLDE---------------VLDNEINRADRYGKNLSLILLDIDHFKEVND 210 Query: 201 QFGHLYGDEVLILVANILRTSFRSHDRIFRFGGEEFVILLRSTTLADASKIFDRFRQHVQ 260 FGH GD VL+ +A ILR + RS D R+GGEEF+++L + DA+++ ++ R ++ Sbjct: 211 NFGHSTGDAVLVRIAEILRANVRSSDLAGRWGGEEFLLILPECDMEDAARMAEKLRLLIE 270 Query: 261 EYDFPQVGKVTVSLGFVGI-SQETPVVILGHADQALYHAKKNGRNRI 306 Y+F VG+ T S G + +L AD ALY AK GRNR+ Sbjct: 271 NYNFVPVGRRTCSFGVAAYQAGHDRTTLLTLADLALYRAKNTGRNRV 317 >gi|300313424|ref|YP_003777516.1| GGDEF domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 372 Score = 100 bits (249), Expect = 2e-22, Method: Compositional matrix adjust. Identities = 65/179 (36%), Positives = 89/179 (49%), Gaps = 28/179 (15%) Query: 141 DALTGLFNRKTFDEQFSRHAFALAPHEAHSLDNNERRNGGETKAHWLAVVDIDHFKQVND 200 D LTG+ NR+ +++ R+ + A +DIDHFK+VND Sbjct: 203 DPLTGVNNRRYIEQRMQEEVA---------------RSQRDRSALSCLFIDIDHFKRVND 247 Query: 201 QFGHLYGDEVLILVANILRTSFRSHDRIFRFGGEEFVILLRSTTLADASKIFDRFRQHVQ 260 QFGH GD+VL VA ++ R D + RFGGEEFV+LL T DA++I +R R V Sbjct: 248 QFGHQSGDDVLREVAARIKKELRLSDALGRFGGEEFVVLLTHATREDAARIAERIRAGVC 307 Query: 261 EYDFPQVG-----KVTVSLGFVGIS--------QETPVVILGHADQALYHAKKNGRNRI 306 G K+T S+G ++ E +L ADQALY AK+ GRNR+ Sbjct: 308 SRGVMIEGSRDPLKITASIGAAALTPPDRSRPAAEVKQAMLKAADQALYQAKEAGRNRV 366 >gi|300312078|ref|YP_003776170.1| hypothetical protein Hsero_2767 [Herbaspirillum seropedicae SmR1] Length = 534 Score = 98.6 bits (244), Expect = 6e-22, Method: Compositional matrix adjust. Identities = 67/186 (36%), Positives = 94/186 (50%), Gaps = 22/186 (11%) Query: 132 QSLLDYSE---RDALTGLFNRKTFDEQFSRHAFALAPHEAHSLDNNERRNGGETKAHWLA 188 Q LL E D LTG NR+ DE R + N RR+ +A Sbjct: 355 QQLLQMGELVREDQLTGSLNRRGMDESLDRE-----------ITNALRRD----TPLCVA 399 Query: 189 VVDIDHFKQVNDQFGHLYGDEVLILVANILRTSFRSHDRIFRFGGEEFVILLRSTTLADA 248 ++D+D FK++ND GH GDEVL+ + ++R + R D I RFGGEEF++L+ T DA Sbjct: 400 LLDLDDFKRINDTHGHATGDEVLVHMVQVIRETLRKLDVIARFGGEEFLVLMPETAPQDA 459 Query: 249 SKIFDRFRQHVQEYDF---PQVGKVTVSLGF-VGISQETPVVILGHADQALYHAKKNGRN 304 +I R ++ + + F Q +T S G V E+ +L AD ALY AK G+N Sbjct: 460 VQIITRVQRELTKRIFMHESQRLLITFSAGVAVYHPGESQADLLKRADVALYKAKNAGKN 519 Query: 305 RICYYD 310 RI + D Sbjct: 520 RIVFAD 525 >gi|300313993|ref|YP_003778085.1| diguanylate cyclase/phosphodiesterase with PAS/PAC sensor domain-containing protein [Herbaspirillum seropedicae SmR1] Length = 573 Score = 97.8 bits (242), Expect = 9e-22, Method: Compositional matrix adjust. Identities = 61/178 (34%), Positives = 94/178 (52%), Gaps = 23/178 (12%) Query: 138 SERDALTGLFNRKTFDEQFSRHAFALAPHEAHSLDNNERRNGGETKAHWLAVVDIDHFKQ 197 S D LTG+ NR+ FDE +L N RR ++ L ++D+D+FK+ Sbjct: 402 SATDGLTGVANRRRFDE---------------ALANEMRRAVRSGQSLALLMLDVDYFKK 446 Query: 198 VNDQFGHLYGDEVLILVANIL-RTSFRSHDRIFRFGGEEFVILLRSTTLADASKIFDRFR 256 ND++GHL GDE L +VA +L ++S R+ D + R+GGEEF +++ A + + Sbjct: 447 YNDRYGHLAGDECLRIVARVLQKSSRRATDLVARYGGEEFSVIIAECDTTQALQQAENIC 506 Query: 257 QHVQEYDFPQV----GKVTVSLGFVGISQE---TPVVILGHADQALYHAKKNGRNRIC 307 Q + E P G ++ S+G + + P ++ ADQALYHAK GRNR+ Sbjct: 507 QAIFELKLPHADSPFGYISASIGVAVLLPDEHTAPEQMVRIADQALYHAKYQGRNRVV 564 Database: BlastDatabases/689/689 Posted date: Apr 10, 2011 12:15 AM Number of letters in database: 1,619,870 Number of sequences in database: 4735 Lambda K H 0.323 0.139 0.423 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 4735 Number of Hits to DB: 1,043,250 Number of extensions: 43847 Number of successful extensions: 196 Number of sequences better than 1.0e-08: 37 Number of HSP's gapped: 134 Number of HSP's successfully gapped: 37 Length of query: 331 Length of database: 1,619,870 Length adjustment: 86 Effective length of query: 245 Effective length of database: 1,212,660 Effective search space: 297101700 Effective search space used: 297101700 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 131 (55.1 bits)